Description Usage Arguments Value
View source: R/AnnotationHelper.R
Annotate "chip.data", given as parameter.
1 2 3 4 | annotate_chip(chip.data, input.chrom.state, tf.regions, histone.regions,
pol.regions, expression.levels, genome.build = c("hg19", "mm9", "mm10",
"hg38"), biosample = "GM12878", tssRegion = c(-3000, 3000), output.dir,
label)
|
chip.data |
A GRanges object containing the ChIP-seq data. |
input.chrom.state |
The name of the file containing the information about chromatin states. |
tf.regions |
A GRangesList object containing the TF regions. |
histone.regions |
A GRangesList object containing the histone regions. |
pol.regions |
A GRangesList object containing the pol2 regions. |
expression.levels |
A data frame containing the levels of expression of genes. according to their EMSEMBL id. |
genome.build |
The name of the chosen annotation ("hg38", "mm9", "mm10", "hg19"). |
biosample |
The biosample identifier from ENCODE. Valid examples are GM12878, K562. |
tssRegion |
A vector with the region range to TSS. |
output.dir |
The name of the directory where to write the selected annotations. |
label |
The name of the file containing all annotation. |
The annotated "chip.data
".
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